In order to use DDT, you just need to convert URLs that point to your content to equivalent links that not only provide the content you intended to provide, but that also let Piwik know that the download has occurred.
For instance, if the link to convert is http://www.mydomain.com/files/document.pdf and the file download.php has been installed in the folder files of root_folder (the root folder of your web server), the new link would be http://www.mydomain.com/files/download.php?file=document.pdf.
However, in case download.php has been installed at the root of the web server (i.e. instead of being installed in files folder) the new link would be http://www.mydomain.com/download.php?file=document.pdf.
In all cases, the new link must match the root_folder path that you will have specified when following the instructions in the Installation section of this webpage. Both the path to download.php and the path to the file to be downloaded must be correct.